User: Rory Stark

gravatar for Rory Stark
Rory Stark2.9k
Reputation:
2,910
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Location:
CRUK, Cambridge, UK
Last seen:
1 week ago
Joined:
6 years, 9 months ago
Email:
r*********@cruk.cam.ac.uk

I am Principal Scientist, Computational Biology at the University of Cambridge, leading the Analysis Team in the Bioinformatics Core at Cancer Research UK's Cambridge Institute.

Posts by Rory Stark

<prev • 511 results • page 1 of 52 • next >
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Answer: A: DiffBind block not working for me
... When you add a blocking contrast, `DiffBind` runs two different analyses: one with and one without the blocking factor. By default, when you call `dba.report()`, you get the non-blocked analysis. You have to request the blocked results using the `method` parameter. To retrieve the results for the b ...
written 7 days ago by Rory Stark2.9k
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Answer: A: How to decide on genes linked by differential binding peaks in opposite conditio
... We currently don't have reliable methods for mapping between ChIP-seq peaks and the genes they regulate (except possibly if they happen to binding inside of an annotated promoter). Some of the peaks may be non-functional, and we don't know which of the "nearby" genes inter-genic binding sites regula ...
written 20 days ago by Rory Stark2.9k
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Answer: A: DiffBind without replicates
... Yes, replicates are required to do any kind of statistical analysis. Replicates are required to estimate the variance in the data and calculate confidence statistics such as p-values/FDRs. Without replicates, you can do some exploratory analysis of overlapping peaks (occupancy analysis). For exampl ...
written 20 days ago by Rory Stark2.9k
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Answer: A: DiffBind minOverlap parameter
... You can make the consensus peakset in two steps: first making a consensus for each sample group with minOverlap=2, then taking the union of these with minOverlap=1. Here's an example using the sample data, where we get the peaks that overlap in at least two of the Responsive samples and at least tw ...
written 20 days ago by Rory Stark2.9k
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Answer: A: Filtering counts in SummarizedExperiment
... You can do this using `dba.count()` by setting `filter=100` and `filterFun=min`. You'll end up filtering out most of your peaks -- if there are any single samples with low binding the site will be removed. ...
written 21 days ago by Rory Stark2.9k
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Comment: C: diffbind plotVenn by Factor
... Check the code snippet I included against yours. I included a call to `dba.peakset()` followed by one to `dba.plotVenn()`. ...
written 21 days ago by Rory Stark2.9k
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Answer: A: in diffbind dba.peakset what is the meaning of minOverlap?
... Generally speaking, occupancy analyses are best performed on the peak data, before calling `dba.count()`. A log2 Fold value of 1 represent a 2-fold change in binding. ...
written 21 days ago by Rory Stark2.9k
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Answer: A: dba.count filter example in manual
... I don't think there is any deep principle underlying the choice of 125, this is just an example in the man page to show how to look at the impact of different filters then how to apply a filter. In my own work I am more likely to use a `max` filter with a much lower threshold (10 or 20), so I filt ...
written 21 days ago by Rory Stark2.9k
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Answer: A: Diffbind with age as blocking factor
... For the first question you should check if the analysis actually identified differentially bound sites with a high confidence. Just because you expect there to be DB sites based on the biology, you may not get the result you expect from the statistical analysis (for example, if there is high varianc ...
written 21 days ago by Rory Stark2.9k
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Answer: A: Is it possible to change how DiffBind merge peaks?
... We are looking at exposing this feature in `DiffBind`, but currently there is no way to override the 1bp overlap. If you are able to separately derive a merged consensus set using alternative criteria, not that you can pass it in to `dba.count()` and that set will be used for all the subsequent ste ...
written 5 weeks ago by Rory Stark2.9k

Latest awards to Rory Stark

Scholar 3 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Scholar 10 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: diffbind finding not differential site
Popular Question 10 months ago, created a question with more than 1,000 views. For diffbind
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Differential analysis of multiple samples with different time points
Popular Question 10 months ago, created a question with more than 1,000 views. For DiffBind & Chip-exo
Scholar 10 months ago, created an answer that has been accepted. For A: dba.count binding matrix coordinates
Popular Question 10 months ago, created a question with more than 1,000 views. For DiffBind annotation
Popular Question 10 months ago, created a question with more than 1,000 views. For DiffBind Question
Scholar 10 months ago, created an answer that has been accepted. For A: DiffBind differential binding normalization with different levels of binding
Popular Question 10 months ago, created a question with more than 1,000 views. For Diffbind: Binding Affinity Heatmap
Popular Question 12 months ago, created a question with more than 1,000 views. For diffbind
Scholar 12 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Scholar 13 months ago, created an answer that has been accepted. For A: DiffBind differential binding normalization with different levels of binding
Scholar 13 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Work with GRanges objects in DiffBind
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Differential analysis of multiple samples with different time points
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: diffbind finding not differential site
Scholar 14 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Scholar 17 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Popular Question 2.4 years ago, created a question with more than 1,000 views. For DiffBind Question
Commentator 2.4 years ago, created a comment with at least 3 up-votes. For C: Diffbind - What exactly is a "consensus" peak set?
Scholar 2.4 years ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Scholar 2.4 years ago, created an answer that has been accepted. For A: DiffBind matrix of values
Popular Question 2.4 years ago, created a question with more than 1,000 views. For diffbind

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